A protocol for adding knowledge to Wikidata, a case report

Andra Waagmeester; Egon L. Willighagen; Andrew I. Su; Martina Kutmon; Jose Emilio Labra Gayo; Daniel Fernández-Álvarez; Peter J. Schaap; Lisa M. Verhagen; Jasper J. Koehorst

Although the RDF data model is very flexible, specifying an agreed structure for the data allows domain experts to identify the properties and structure of their data facilitating the integration between heterogeneous data sources. Shape expressions were used to provide the right level of abstraction. YaShE, a ShEx editor implemented in JavaScript, was applied to author these shapes (32) . This application provides the means to associate labels in the natural language of Wikidata to the corresponding identifiers. The initial entity schema was defined with YaShE as a proof of concept for virus genes and proteins. In parallel, statements already available in Wikidata were used to automatically generate an initial shape for virus strains with sheXer. The statements for virus strains were retrieved with SPARQL 6 . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.05.026336 doi: bioRxiv preprint from the Wikidata Query Service (WDQS). The generated shape was then further improved through manual curation. The syntax of the shape expressions were continuously validated through YaShE and the Wikidata Entity Schema namespace was used to share and collaboratively update the schema with new properties. Figure 3 gives a visual outline of these steps.